Editing Urease

{{Short description|Multiprotein Nickel-containing complex which hydrolyses urea}}
{{Infobox enzyme
| Name       = Urease
| EC_number  = 3.5.1.5
| CAS_number = 9002-13-5
| GO_code    = 0009039
| name       =
| image      = Urease 2KAU.png
| width      = 
| caption    = 3D model of urease from ''Klebsiella aerogenes'', two Ni<sup>2+</sup>-ions are shown as green spheres.<ref name="pmid28669634">{{PDB|2KAU}}; {{cite journal | vauthors = Jabri E, Carr MB, Hausinger RP, Karplus PA | title = The crystal structure of urease from Klebsiella aerogenes.
 | journal = Science| volume = 268| issue = 5213 | pages = 998–1004 | date = May 1995 | pmid = 7754395| doi = 10.1126/science.7754395| bibcode = 1995Sci...268..998J
 }}</ref> 
}}
'''Ureases''' ({{EC number|3.5.1.5}}), functionally, belong to the [[Protein family|superfamily]] of [[amidohydrolases]] and phosphotriesterases.<ref name="pmid9144792">{{cite journal | vauthors = Holm L, Sander C | title = An evolutionary treasure: unification of a broad set of amidohydrolases related to urease | journal = Proteins | volume = 28 | issue = 1 | pages = 72–82 | year = 1997 | pmid = 9144792 | doi = 10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L | citeseerx = 10.1.1.621.2752 | s2cid = 38845090 }}</ref> Ureases are found in numerous [[Bacteria]], [[Archaea]], [[fungi]], [[algae]], plants, and some [[invertebrates]]. Ureases are nickel-containing [[metalloenzymes]] of high molecular weight.<ref name="Krajewska">{{cite journal | vauthors = Krajewska B, van Eldik R, Brindell M | title = Temperature- and pressure-dependent stopped-flow kinetic studies of jack bean urease. Implications for the catalytic mechanism | journal = Journal of Biological Inorganic Chemistry | volume = 17 | issue = 7 | pages = 1123–1134 | date = 13 August 2012 | pmid = 22890689 | pmc = 3442171 | doi = 10.1007/s00775-012-0926-8 }}</ref> Ureases are distinct from Urecases are important in degrading avian faecal matter, which is rich in uric acid, the breakdown product of which is urea, which is then degraded by urease as described here. 

These [[enzyme]]s [[catalysis|catalyze]] the [[hydrolysis]] of [[urea]] into [[carbon dioxide]] and [[ammonia]]:
: (NH<sub>2</sub>)<sub>2</sub>CO + H<sub>2</sub>O {{overset|urease|→}} CO<sub>2</sub> + 2NH<sub>3</sub>

The hydrolysis of [[urea]] occurs in two stages.  In the first stage, [[ammonia]] and [[carbamic acid]] are produced. The [[carbamate]] spontaneously and rapidly hydrolyzes to [[ammonia]] and [[carbonic acid]].<!--inapprop to cite theory to describe mech foundations:<ref name="Zimmer">{{cite journal | vauthors = Zimmer M | title = Molecular mechanics evaluation of the proposed mechanisms for the degradation of urea by urease | journal = J Biomol Struct Dyn | volume = 17 | issue = 5 | pages = 787–97 | date = Apr 2000 | pmid = 10798524 | doi = 10.1080/07391102.2000.10506568 | url = http://www.tandfonline.com/doi/abs/10.1080/07391102.2000.10506568 }}</ref>--> Urease activity increases the [[pH]] of its environment as ammonia is produced, which is basic.

== History ==
Urease activity was first identified in 1876 by [[Frédéric Alphonse Musculus]] as a soluble ferment.<ref>Musculus, « Sur le ferment de l'urée », Comptes rendus de l'Académie des sciences, vol. 82, 1876, pp. 333-336, reachable in [http://gallica.bnf.fr/ark:/12148/bpt6k30396/f332.image Gallica]</ref> 
In 1926, [[James B. Sumner]], showed that urease is a [[protein]] by examining its crystallized form.<ref name="karplus">{{cite journal | vauthors = Karplus PA, Pearson MA, Hausinger RP | year = 1997 | title = 70 years of crystalline urease: What have we learned? | journal = Accounts of Chemical Research | volume = 30 | issue = 8| pages = 330–337 | doi=10.1021/ar960022j}}</ref> Sumner's work was the first demonstration that a [[protein]] can function as an [[enzyme]] and led eventually to the recognition that most enzymes are in fact proteins. Urease was the first enzyme crystallized. For this work, Sumner was awarded the [[Nobel prize in chemistry]] in 1946.<ref>[https://www.nobelprize.org/nobel_prizes/chemistry/laureates/1946/sumner-bio.html The Nobel Prize in Chemistry 1946]</ref> The crystal structure of urease was first solved by P. A. Karplus in 1995.<ref name="karplus"/>

== Importance ==
Urease is important because of its role in the [[Nitrogen cycle#:~:text=The nitrogen cycle is the,both biological and physical processes.|Nitrogen cycle]] as a key catalyst in the reaction converting urea to ammonium and CO<sub>2</sub>. Urease occurs as a [[soil enzyme]], likely because soil microorganisms benefit from the nitrogen made available by urea degradation in the form of ammonium.<ref>{{Cite journal |last=Demoling |first=Fredrik |last2=Figueroa |first2=Daniela |last3=Bååth |first3=Erland |date=2007-10-01 |title=Comparison of factors limiting bacterial growth in different soils |url=https://www.sciencedirect.com/science/article/abs/pii/S0038071707001939 |journal=Soil Biology and Biochemistry |volume=39 |issue=10 |pages=2485–2495 |doi=10.1016/j.soilbio.2007.05.002 |issn=0038-0717}}</ref> 

==Structure==

A 1984 study focusing on urease from [[jack bean]] found that the [[active site]] contains a pair of [[nickel]] centers.<ref>{{cite journal | pmid = 6398286 | title=Nickel--an essential element | year=1984 | journal=IARC Sci. Publ. | pages=339–65 | vauthors=Anke M, Groppel B, Kronemann H, Grün M | issue=53}}</ref> [[In vitro]] activation also has been achieved with [[manganese]] and [[cobalt]] in place of nickel.<ref name="pmid20046957">{{cite journal | vauthors = Carter EL, Flugga N, Boer JL, Mulrooney SB, Hausinger RP | title = Interplay of metal ions and urease | journal = Metallomics | volume = 1 | issue = 3 | pages = 207–21 | date = 1 January 2009 | pmid = 20046957 | pmc = 2745169 | doi = 10.1039/b903311d }}</ref>  Lead salts are [[Enzyme inhibitor|inhibiting]].

The [[molecular weight]] is either 480 [[Atomic mass unit|kDa]] or 545 [[Atomic mass unit|kDa]] for jack-bean urease (calculated mass from the amino acid sequence). 840 amino acids per molecule, of which 90 are cysteine residues.<ref name="Molecular Catalysis B 2009">{{cite journal| vauthors = Krajewska B |title=Ureases I. Functional, catalytic and kinetic properties: A review|journal=Journal of Molecular Catalysis B: Enzymatic|date=30 June 2009|volume=59|issue=1–3|pages=9–21|doi=10.1016/j.molcatb.2009.01.003}}</ref>

The optimum [[pH]] is 7.4 and optimum temperature is 60&nbsp;°C.  Substrates include urea and [[hydroxyurea]].

Bacterial ureases are composed of three distinct subunits, one large catalytic (α 60–76kDa) and two small (β 8–21 kDa, γ 6–14 kDa) commonly forming (αβγ)<sub>3</sub> trimers [[stoichiometry]] with a 2-fold symmetric structure (note that the image above gives the structure of the asymmetric unit, one-third of the true biological assembly), they are cysteine-rich enzymes, resulting in the enzyme molar masses between 190 and 300kDa.<ref name="Molecular Catalysis B 2009"/>

An exceptional urease is obtained from ''Helicobacter'' sp..  These are composed of two subunits, α(26–31 kDa)-β(61–66 kDa).  These subunits form a supramolecular (αβ)<sub>12</sub> [[dodecameric]] complex.<ref name="pmid11373617">{{cite journal | vauthors = Ha NC, Oh ST, Sung JY, Cha KA, Lee MH, Oh BH | title = Supramolecular assembly and acid resistance of Helicobacter pylori urease | journal = Nature Structural Biology | volume = 8 | issue = 6 | pages = 505–509 | date = 31 May 2001 | pmid = 11373617 | doi = 10.1038/88563 | s2cid = 26548257 }}</ref> of repeating α-β subunits, each coupled pair of subunits has an active site, for a total of 12 active sites.<ref name="pmid11373617" /> It plays an essential function for survival, neutralizing [[gastric acid]] by allowing [[urea]] to enter into [[periplasm]] via a [[proton-gated urea channel]].<ref name="pmid23222544">{{cite journal | vauthors = Strugatsky D, McNulty R, Munson K, Chen CK, Soltis SM, Sachs G, Luecke H | title = Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori | journal = Nature | volume = 493 | issue = 7431 | pages = 255–258 | date = 8 December 2012 | pmid = 23222544 | doi = 10.1038/nature11684 | pmc=3974264}}</ref> The presence of urease is used in the diagnosis of ''[[Helicobacter]]'' species.

All bacterial ureases are solely cytoplasmic, except for those in ''Helicobacter pylori'', which along with its cytoplasmic activity, has external activity with host cells. In contrast, all plant ureases are cytoplasmic.<ref name="Molecular Catalysis B 2009"/>

Fungal and plant ureases are made up of identical subunits (~90 kDa each), most commonly assembled as trimers and hexamers. For example, jack bean urease has two structural and one catalytic subunit. The α subunit contains the active site, it is composed of 840 amino acids per molecule (90 cysteines), its molecular mass without Ni(II) ions amounting to 90.77 kDa. The mass of the [[hexamer]] with the 12 nickel ions is 545.34 kDa. Other examples of homohexameric structures of plant ureases are those of soybean, pigeon pea and cotton seeds enzymes.<ref name="Molecular Catalysis B 2009"/>

It is important to note, that although composed of different types of subunits, ureases from different sources extending from bacteria to plants and fungi exhibit high homology of amino acid sequences. The single plant urease chain is equivalent to a fused γ-β-α organization. The ''Helicobacter'' "α" is equivalent to a fusion of the normal bacterial γ-β subunits, while its "β" subunit is equivalent to the normal bacterial α.<ref name="Molecular Catalysis B 2009"/> The three-chain organization is likely ancestral.<ref name="pmid30094078">{{cite journal |last1=Kappaun |first1=K |last2=Piovesan |first2=AR |last3=Carlini |first3=CR |last4=Ligabue-Braun |first4=R |title=Ureases: Historical aspects, catalytic, and non-catalytic properties - A review. |journal=Journal of Advanced Research |date=September 2018 |volume=13 |pages=3–17 |doi=10.1016/j.jare.2018.05.010 |pmid=30094078 |pmc=6077230 |doi-access=free}}</ref>

==Activity==

The ''k''<sub>cat</sub>/''K''<sub>m</sub> of urease in the processing of [[urea]] is 10<sup>14</sup> times greater than the rate of the uncatalyzed elimination reaction of [[urea]].<ref name="karplus"/> There are many reasons for this observation in nature. The proximity of [[urea]] to active groups in the active site along with the correct orientation of urea allow [[hydrolysis]] to occur rapidly. [[Urea]] alone is very stable due to the resonance forms it can adopt. The stability of urea is understood to be due to its [[resonance]] energy, which has been estimated at 30–40 kcal/mol.<ref name="karplus"/> This is because the [[zwitterionic]] resonance forms all donate electrons to the [[carbonyl]] carbon making it less of an [[electrophile]] making it less reactive to nucleophilic attack.<ref name="karplus"/>

===Active site===

The [[active site]] of ureases is located in the α (alpha) [[Protein subunit|subunits]]. It is a bis-μ-hydroxo dimeric [[nickel]] center, with an interatomic distance of ~3.5 Å.<ref name="karplus" /> > The Ni(II) pair are weakly [[Antiferromagnetism|antiferromagnetically]] coupled.<ref>{{cite journal | vauthors = Ciurli S, Benini S, Rypniewski WR, Wilson KS, Miletti S, Mangani S | title = Structural properties of the nickel ions in urease: novel insights into the catalytic and inhibition mechanisms | journal = Coordination Chemistry Reviews | year = 1999 | volume = 190–192 | pages = 331–355 | doi = 10.1016/S0010-8545(99)00093-4 }}</ref> [[X-ray absorption spectroscopy]] (XAS) studies of ''[[Canavalia ensiformis]]''  (jack bean), ''Klebsiella aerogenes''  and ''[[Sporosarcina pasteurii]]'' (formerly known as ''Bacillus pasteurii'')<ref name="Benini, S. 1999"/> confirm 5–6 coordinate nickel ions with exclusively O/N ligation, including two [[imidazole]] ligands per nickel.<ref name="pmid20046957" /> Urea substrate is proposed to displace [[aquo ligand]]s.

Water molecules located towards the opening of the active site form a tetrahedral cluster that fills the cavity site through [[hydrogen bonds]].  Some amino acid residues are proposed to form mobile flap of the site, which gate for the substrate.<ref name="Krajewska" /> Cysteine residues are common in the flap region of the enzymes, which have been determined not to be essential in catalysis, although involved in positioning other key residues in the active site appropriately.<ref name="Martin">{{cite journal | vauthors = Martin PR, Hausinger RP | title = Site-directed mutagenesis of the active site cysteine in ''Klebsiella aerogenes'' urease | journal = The Journal of Biological Chemistry | volume = 267 | issue = 28 | pages = 20024–7 | date = Oct 5, 1992 | doi = 10.1016/S0021-9258(19)88659-3 | pmid = 1400317 | doi-access = free }}</ref> In ''[[Sporosarcina pasteurii]]'' urease, the flap was found in the open conformation, while its closed conformation is apparently needed for the reaction.<ref name="Benini, S. 1999">{{cite journal | vauthors = Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S | title = A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels | journal = Structure | volume = 7 | issue = 2 | pages = 205–216 | date = 31 January 1999 | pmid = 10368287 | doi = 10.1016/S0969-2126(99)80026-4 | doi-access = free }}</ref>

When compared, the α subunits of ''[[Helicobacter pylori]]'' urease and other bacterial ureases align with the jack bean ureases.<ref name="Martin" />

The binding of urea to the active site of urease has not been observed.<ref name="Molecular Catalysis B 2009"/>

===Proposed mechanisms===

====Blakeley/Zerner====

One mechanism for the catalysis of this reaction by urease was proposed by Blakely and Zerner.<ref name="pmid6788353">{{cite journal | vauthors = Dixon NE, Riddles PW, Gazzola C, Blakeley RL, Zerner B | title = Jack Jack Bean Urease (EC3.5.1.5). V. On the Mechanism of action of urease on urea, formamide, acetamide,N-methylurea, and related compounds | journal = Canadian Journal of Biochemistry | volume = 58 | issue = 12 | pages = 1335–1344 | year = 1979 | pmid = 6788353 | doi = 10.1139/o80-181 }}</ref> It begins with a nucleophilic attack by the [[carbonyl]] oxygen of the [[urea]] molecule onto the 5-coordinate Ni (Ni-1). A weakly coordinated water ligand is displaced in its place. A lone pair of electrons from one of the nitrogen atoms on the [[Urea]] molecule creates a double bond with the central carbon, and the resulting NH<sub>2</sub><sup>−</sup> of the coordinated substrate interacts with a nearby positively charged group. Blakeley and Zerner proposed this nearby group to be a [[Carboxylate|Carboxylate ion]], although deprotonated carboxylates are negatively charged.

A hydroxide ligand on the six coordinate Ni is deprotonated by a base. The carbonyl carbon is subsequently attacked by the electronegative oxygen. A pair of electrons from the nitrogen-carbon double bond returns to the nitrogen and neutralizes the charge on it, while the now 4-coordinate carbon assumes an intermediate tetrahedral orientation.

The breakdown of this intermediate is then helped by a sulfhydryl group of a [[cysteine]] located near the active site. A hydrogen bonds to one of the nitrogen atoms, breaking its bond with carbon, and releasing an {{NH3}} molecule.  Simultaneously, the bond between the oxygen and the 6-coordinate nickel is broken. This leaves a carbamate ion coordinated to the 5-coordinate Ni, which is then displaced by a water molecule, regenerating the enzyme.

The [[carbamate]] produced then spontaneously degrades to produce another ammonia and [[carbonic acid]].<ref name="Zimmer">{{cite journal | vauthors = Zimmer M | title = Molecular mechanics evaluation of the proposed mechanisms for the degradation of urea by urease | journal = J Biomol Struct Dyn | volume = 17 | issue = 5 | pages = 787–97 | date = Apr 2000 | pmid = 10798524 | doi = 10.1080/07391102.2000.10506568 | s2cid = 41497756 }}</ref>

====Hausinger/Karplus====

The mechanism proposed by Hausinger and Karplus attempts to revise some of the issues apparent in the Blakely and Zerner pathway, and focuses on the positions of the side chains making up the urea-binding pocket.<ref name="karplus"/>  From the crystal structures from ''K. aerogenes'' urease, it was argued that the general base used in the Blakely mechanism, His<sup>320</sup>, was too far away from the Ni2-bound water to deprotonate in order to form the attacking hydroxide moiety.  In addition, the general acidic ligand required to protonate the urea nitrogen was not identified.<ref name="Jabri">{{cite journal | vauthors = Jabri E, Carr MB, Hausinger RP, Karplus PA | title = The crystal structure of urease from Klebsiella aerogenes | journal = Science | volume = 268 | issue = 5213 | pages = 998–1004 | date = May 19, 1995 | pmid = 7754395 | doi = 10.1126/science.7754395 | bibcode = 1995Sci...268..998J }}</ref> Hausinger and Karplus suggests a reverse protonation scheme, where a protonated form of the His<sup>320</sup> ligand plays the role of the general acid and the Ni2-bound water is already in the deprotonated state.<ref name="karplus"/>  The mechanism follows the same path, with the general base omitted (as there is no more need for it) and His<sup>320</sup> donating its proton to form the ammonia molecule, which is then released from the enzyme.  While the majority of the His<sup>320</sup> ligands and bound water will not be in their active forms (protonated and deprotonated, respectively,) it was calculated that approximately 0.3% of total urease enzyme would be active at any one time.<ref name="karplus"/>  While logically, this would imply that the enzyme is not very efficient, contrary to established knowledge, usage of the reverse protonation scheme provides an advantage in increased reactivity for the active form, balancing out the disadvantage.<ref name="karplus"/>  Placing the His<sup>320</sup> ligand as an essential component in the mechanism also takes into account the mobile flap region of the enzyme.  As this histidine ligand is part of the mobile flap, binding of the urea substrate for catalysis closes this flap over the active site and with the addition of the hydrogen bonding pattern to urea from other ligands in the pocket, speaks to the selectivity of the urease enzyme for urea.<ref name="karplus"/>

====Ciurli/Mangani====

The mechanism proposed by Ciurli and Mangani<ref name="pmid21542631">{{cite journal | vauthors = Zambelli B, Musiani F, Benini S, Ciurli S | title = Chemistry of Ni2+ in Urease: Sensing, Trafficking, and Catalysis | journal = Accounts of Chemical Research | volume = 44 | issue = 7 | pages = 520–530 | date = 19 July 2011 | pmid = 21542631 | doi = 10.1021/ar200041k }}</ref> is one of the more recent and currently accepted views of the mechanism of urease and is based primarily on the different roles of the two [[nickel]] ions in the active site.<ref name="Benini, S. 1999" /> One of which binds and activates urea, the other nickel ion binds and activates the nucleophilic water molecule.<ref name="Benini, S. 1999"/>  With regards to this proposal, urea enters the active site cavity when the mobile ‘flap’ (which allows for the entrance of urea into the active site) is open. Stability of the binding of urea to the active site is achieved via a [[hydrogen-bonding]] network, orienting the substrate into the catalytic cavity.<ref name="Benini, S. 1999"/>  Urea binds to the five-coordinated nickel (Ni1) with the carbonyl [[oxygen]] atom. It approaches the six-coordinated nickel (Ni2) with one of its amino groups and subsequently bridges the two nickel centers.<ref name="Benini, S. 1999"/>  The binding of the urea carbonyl oxygen atom to Ni1 is stabilized through the protonation state of His<sup>α222</sup> Nԑ. Additionally, the conformational change from the open to closed state of the mobile flap generates a rearrangement of Ala<sup>α222</sup> carbonyl group in such a way that its oxygen atom points to Ni2.<ref name="Benini, S. 1999"/>  The Ala<sup>α170</sup> and Ala<sup>α366</sup> are now oriented in a way that their carbonyl groups act as hydrogen-bond acceptors towards NH<sub>2</sub> group of urea, thus aiding its binding to Ni2.<ref name="Benini, S. 1999"/>  Urea is a very poor [[chelating ligand]] due to low [[Lewis base]] character of its NH<sub>2</sub> groups. However the carbonyl oxygens of Ala<sup>α170</sup> and Ala<sup>α366</sup> enhance the basicity of the NH<sub>2</sub> groups and allow for binding to Ni2.<ref name="Benini, S. 1999"/> Therefore, in this proposed mechanism, the positioning of urea in the active site is induced by the structural features of the active site residues which are positioned to act as hydrogen-bond donors in the vicinity of Ni1 and as acceptors in the vicinity of Ni2.<ref name="Benini, S. 1999"/>  The main structural difference between the Ciurli/Mangani mechanism and the other two is that it incorporates a [[nitrogen]], oxygen bridging urea that is attacked by a bridging [[hydroxide]].<ref name=Zimmer />

===Action in pathogenesis===

Bacterial ureases are often the mode of [[pathogenesis]] for many medical conditions. They are associated with [[hepatic encephalopathy]] / [[Hepatic coma]], infection stones, and peptic ulceration.<ref name="mobley">{{cite journal | vauthors = Mobley HL, Hausinger RP | title = Microbial ureases: significance, regulation, and molecular characterization | journal = Microbiological Reviews | volume = 53 | issue = 1 | pages = 85–108 | date = March 1989 | doi = 10.1128/MMBR.53.1.85-108.1989 | pmid = 2651866 | pmc = 372718 }}</ref>

====Infection stones====

Infection induced urinary stones are a mixture of [[struvite]] (MgNH<sub>4</sub>PO<sub>4</sub>•6H<sub>2</sub>O) and [[carbonate]] [[apatite]] [Ca<sub>10</sub>(PO<sub>4</sub>)6•CO<sub>3</sub>].<ref name="mobley"/> These polyvalent ions are soluble but become insoluble when [[ammonia]] is produced from microbial urease during [[urea]] [[hydrolysis]], as this increases the surrounding environments [[pH]] from roughly 6.5 to 9.<ref name="mobley"/> The resultant alkalinization results in stone [[crystallization]].<ref name="mobley"/> In humans the microbial urease, ''Proteus mirabilis'', is the most common in infection induced urinary stones.<ref name="pmid3524996">{{cite journal | vauthors = Rosenstein IJ | title = Urinary Calculi: Microbiological and Crystallographic Studies | journal = Critical Reviews in Clinical Laboratory Sciences | volume = 23 | issue = 3 | pages = 245–277 | date = 1 January 1986 | pmid = 3524996 | doi = 10.3109/10408368609165802 }}</ref>

====Urease in hepatic encephalopathy / hepatic coma====

Studies have shown that ''[[Helicobacter pylori]]'' along with [[cirrhosis]] of the liver cause [[hepatic encephalopathy]] and [[hepatic coma]].<ref name="agrawal">{{cite journal | vauthors = Agrawal A, Gupta A, Chandra M, Koowar S | title = Role of Helicobacter pylori infection in the pathogenesis of minimal hepatic encephalopathy and effect of its eradication | journal = Indian Journal of Gastroenterology | volume = 30 | issue = 1 | pages = 29–32 | date = 17 March 2011 | pmid = 21416318 | doi = 10.1007/s12664-011-0087-7 | s2cid = 25452909 }}</ref> ''Helicobacter pylori''  release microbial ureases into the stomach. The urease hydrolyzes [[urea]] to produce [[ammonia]] and [[carbonic acid]]. As the bacteria are localized to the stomach [[ammonia]] produced is readily taken up by the [[circulatory system]] from the gastric [[lumen (anatomy)|lumen]].<ref name="agrawal"/> This results in elevated [[ammonia]] levels in the blood, a condition known as [[hyperammonemia]]; eradication of ''Helicobacter pylori'' show marked decreases in [[ammonia]] levels.<ref name="agrawal"/>

====Urease in peptic ulcers====

''Helicobacter pylori'' is also the cause of peptic ulcers with its manifestation in 55–68% reported cases.<ref name="tang">{{cite journal | vauthors = Tang JH, Liu NJ, Cheng HT, Lee CS, Chu YY, Sung KF, Lin CH, Tsou YK, Lien JM, Cheng CL | title = Endoscopic diagnosis of Helicobacter pylori infection by rapid urease test in bleeding peptic ulcers: a prospective case-control study | journal = Journal of Clinical Gastroenterology | volume = 43 | issue = 2 | pages = 133–9 | date = February 2009 | pmid = 19230239 | doi = 10.1097/MCG.0b013e31816466ec | s2cid = 27784917 }}</ref>  This was confirmed by decreased [[ulcer]] bleeding and [[ulcer]] reoccurrence after eradication of the [[pathogen]].<ref name="tang"/> In the stomach there is an increase in [[pH]] of the mucosal lining as a result of [[urea]] [[hydrolysis]], which prevents movement of [[hydrogen ions]] between gastric glands and gastric [[lumen (anatomy)|lumen]].<ref name="mobley"/>  In addition, the high [[ammonia]] concentrations have an effect on intercellular [[tight junctions]] increasing permeability and also disrupting the gastric [[mucous membrane]] of the stomach.<ref name="mobley"/><ref>{{cite journal | vauthors = Caron TJ, Scott KE, Fox JG, Hagen SJ | title = Tight junction disruption: Helicobacter pylori and dysregulation of the gastric mucosal barrier | journal = World Journal of Gastroenterology | volume = 21 | issue = 40 | pages = 11411–27 | date = October 2015 | pmid = 26523106 | pmc = 4616217 | doi = 10.3748/wjg.v21.i40.11411 | doi-access = free }}</ref>

==Occurrence and applications in agriculture==
Urea is found naturally in the environment and is also artificially introduced, comprising more than half of all synthetic nitrogen fertilizers used globally.<ref>{{cite journal | vauthors = Glibert P, Harrison J, Heil C, Seitzinger S | year = 2006 | title = Escalating worldwide use of urea – a global change contributing to coastal eutrophication | journal = Biogeochemistry | volume = 77 | issue = 3| pages = 441–463 | doi=10.1007/s10533-005-3070-5| s2cid = 2209850 }}</ref>  Heavy use of urea is thought to promote [[eutrophication]], despite the observation that urea is rapidly transformed by microbial ureases, and thus usually does not persist.<ref>{{cite journal | vauthors = Daigh AL, Savin MC, Brye K, Norman R, Miller D | year = 2014 | title = Urea persistence in floodwater and soil used for flooded rice production | journal = Soil Use and Management | volume = 30 | issue = 4| pages = 463–470 | doi = 10.1111/sum.12142 | s2cid = 97961385 }}</ref>   Environmental urease activity is often measured as an indicator of the health of microbial communities.  In the absence of plants, urease activity in soil is generally attributed to heterotrophic microorganisms, although it has been demonstrated that some chemoautotrophic ammonium oxidizing bacteria are capable of growth on urea as a sole source of carbon, nitrogen, and energy.<ref>{{cite journal | vauthors = Marsh KL, Sims GK, Mulvaney RL | title = Availability of urea to autotrophic ammonia-oxidizing bacteria as related to the fate of 14 C-and 15 N-labeled urea added to soil. | journal = Biology and Fertility of Soils. | date = November 2005 | volume = 42 | issue = 2 | pages = 137–145 | doi = 10.1007/s00374-005-0004-2 | s2cid = 6245255 }}</ref>

=== Inhibition in fertilizers ===
{{Further|Controlled release fertilizer|Ammonia volatilization from urea}}
The inhibition of urease is a significant goal in agriculture because the rapid breakdown of urea-based fertilizers is wasteful and environmentally damaging.<ref name=Pan>{{cite journal | vauthors = Pan B, Lam SK, Mosier A, Luo Y, Chen D |title=Ammonia Volatilization from Synthetic Fertilizers and its Mitigation Strategies: A Global Synthesis|year=2016 |journal=Agriculture, Ecosystems & Environment|volume=232|pages=283–289 |doi=10.1016/j.agee.2016.08.019 }}</ref>  [[Phenyl phosphorodiamidate]] and [[N-(n-butyl)thiophosphoric triamide|''N''-(''n''-butyl)thiophosphoric triamide]] are two such inhibitors.<ref>{{cite journal | vauthors = Gholivand K, Pooyan M, Mohammadpanah F, Pirastefar F, Junk PC, Wang J, Ebrahimi Valmoozi AA, Mani-Varnosfaderani A | display-authors = 6 | title = Synthesis, crystal structure and biological evaluation of new phosphoramide derivatives as urease inhibitors using docking, QSAR and kinetic studies | journal = Bioorganic Chemistry | volume = 86 | pages = 482–493 | date = May 2019 | pmid = 30772649 | doi = 10.1016/j.bioorg.2019.01.064 | s2cid = 73460771 }}</ref>

===Biomineralization===
By promoting the formation of [[calcium carbonate]], ureases are potentially useful for [[biomineralization]]-inspired processes.<ref>{{cite journal | vauthors = Anbu P, Kang CH, Shin YJ, So JS | title = Formations of calcium carbonate minerals by bacteria and its multiple applications | journal = SpringerPlus | volume = 5 | pages = 250 | date = 1 March 2016 | pmid = 27026942 | pmc = 4771655 | doi = 10.1186/s40064-016-1869-2 | doi-access = free }}</ref> Notably, microbiologically induced formation of calcium carbonate can be used in making [[bioconcrete]].<ref>{{cite web| vauthors = Moneo S |title=Dutch scientist invents self-healing concrete with bacteria|url=https://canada.constructconnect.com/joc/news/Infrastructure/2015/9/Dutch-scientist-invents-self-healing-concrete-with-bacteria-1010047W|website=Journal Of Commerce|access-date=23 March 2018|date=11 September 2015}}</ref>

== Non-enzymatic action ==
In addition to acting as an enzyme, some ureases (especially plant ones) have additional effects that persist even when the catalytic function is disabled. These include entomotoxicity, inhibition of fungi, [[neurotoxicity]] in mammals, promotion of endocytosis and inflammatory eicosanoid production in mammals, and induction of [[chemotaxis]] in bacteria. These activities may be part of a defense mechanism.<ref name="pmid30094078"/>

Urease insect-toxicity was originally noted in canatoxin, an orthologous isoform of jack bean urease. Digestion of the peptide identified a 10-kDa portion most responsible for this effect, termed jaburetox. An analogous portion from the soybean urease is named soyuretox. Studies on insects show that the entire protein is toxic without needing any digestion, however. Nevertheless, the "uretox" peptides, being more concentrated in toxicity, show promise as [[biopesticide]]s.<ref name="pmid30094078"/>

== As diagnostic test ==
{{Main|Rapid urease test}}
Many gastrointestinal or urinary tract pathogens produce urease, enabling the detection of urease to be used as a diagnostic to detect presence of pathogens.

Urease-positive pathogens include:
*''[[Proteus mirabilis]]'' and ''[[Proteus vulgaris]]''
*''[[Ureaplasma urealyticum]]'', a relative of ''[[Mycoplasma]]'' spp.
*''[[Nocardia]]''
*''[[Corynebacterium urealyticum]]''
*''[[Cryptococcus (fungus)|Cryptococcus]]'' spp., an [[opportunistic infection|opportunistic]] fungus
*''[[Helicobacter pylori]]''
*Certain [[Enteric bacteria]] including ''[[Proteus (bacterium)|Proteus]]'' spp., ''[[Klebsiella]]'' spp., ''[[Morganella (bacterium)|Morganella]]'', ''[[Providencia (bacterium)|Providencia]]'', and possibly ''[[Serratia]]'' spp.
*''[[Brucella]]''
* ''[[Staphylococcus saprophyticus]]''
* ''[[Staphylococcus aureus]]''<ref name="pmid30608981">{{cite journal | vauthors = Zhou C, Bhinderwala F, Lehman MK, Thomas VC, Chaudhari SS, Yamada KJ, Foster KW, Powers R, Kielian T, Fey PD | display-authors = 6 | title = Urease is an essential component of the acid response network of Staphylococcus aureus and is required for a persistent murine kidney infection | journal = PLOS Pathogens | volume = 15 | issue = 1 | pages = e1007538 | date = January 2019 | pmid = 30608981 | pmc = 6343930 | doi = 10.1371/journal.ppat.1007538 | doi-access = free }}</ref>

== Ligands ==

=== Inhibitors ===
A wide range of urease inhibitors of different structural families are known. Inhibition of urease is not only of interest to agriculture, but also to medicine as pathogens like ''[[H. pylori]]'' produce urease as a survival mechanism. Known structural classes of inhibitors include:<ref>{{cite journal |last1=Modolo |first1=LV |last2=da-Silva |first2=CJ |last3=Brandão |first3=DS |last4=Chaves |first4=IS |title=A minireview on what we have learned about urease inhibitors of agricultural interest since mid-2000s. |journal=Journal of Advanced Research |date=September 2018 |volume=13 |pages=29–37 |doi=10.1016/j.jare.2018.04.001 |pmid=30094080 |pmc=6077229 |doi-access=free}}</ref><ref>{{cite journal |last1=Kafarski |first1=P |last2=Talma |first2=M |title=Recent advances in design of new urease inhibitors: A review. |journal=Journal of Advanced Research |date=September 2018 |volume=13 |pages=101–112 |doi=10.1016/j.jare.2018.01.007 |pmid=30094085 |pmc=6077125 |doi-access=free}}</ref>

* Analogues of urea, the strongest being [[thiourea]]s like 1-(4-chlorophenyl)-3-palmitoylthiourea.
* Phosphoramidates, the most commonly used in agriculture (see above).
* Hydroquinone and quinones. In medicine, the most interesting are [[Quinolone antibiotics|quinolones]], already a class of widely used antibiotics.
* Some plant metabolites are also urease inhibitors, an example being [[allicin]]. These have potential both as environmentally-friendly fertilizer additives<ref>{{cite journal |last1=Ee Huey |first1=Choo |last2=Zaireen Nisa Yahya |first2=Wan |last3=Mansor |first3=Nurlidia |title=Allicin incorporation as urease inhibitor in a chitosan/starch based biopolymer for fertilizer application |journal=Materials Today: Proceedings |date=2019 |volume=16 |pages=2187–2196 |doi=10.1016/j.matpr.2019.06.109|s2cid=202073615 }}</ref> and natural drugs.

==Extraction==
{{missing information|applications of urease|date=May 2022}}
First isolated as a crystal in 1926 by Sumner, using acetone solvation and centrifuging.<ref>{{cite journal| vauthors = Gorin G, Butler MF, Katyal JM, Buckley JE |title=Isolation of crystalline urease |journal=Proceedings of the Oklahoma Academy of Science |date=1959 |volume=40 |pages=62–70 |url=http://digital.library.okstate.edu/oas/oas_pdf/v40/p62_70.pdf|access-date=Dec 7, 2014}}</ref> Modern biochemistry has increased its demand for urease. [[jack bean|Jack bean meal]],<ref>{{cite journal | vauthors = Sung HY, Lee WM, Chiou MJ, Chang CT | title = A procedure for purifying jack bean urease for clinical use | journal = Proceedings of the National Science Council, Republic of China. Part B, Life Sciences | volume = 13 | issue = 4 | pages = 250–7 | date = October 1989 | pmid = 2517764 }}</ref> [[Watermelon|watermelon seeds]],<ref>{{cite journal | vauthors = Prakash O, Bhushan G |title=Isolation, purification and partial characterisation of urease from seeds of water melon (''Citrullus vulgaris'')|journal=Journal of Plant Biochemistry and Biotechnology|date= January 1997|volume=6|pages=45–47|doi=10.1007/BF03263009|s2cid=41143649 }}</ref> and [[pea|pea seeds]]<ref>{{cite journal | vauthors = El-Hefnawy ME, Sakran M, Ismail AI, Aboelfetoh EF | title = Extraction, purification, kinetic and thermodynamic properties of urease from germinating ''Pisum sativum'' L. seeds | journal = BMC Biochemistry | volume = 15 | issue = 1 | pages = 15 | date = July 2014 | pmid = 25065975 | pmc = 4121304 | doi = 10.1186/1471-2091-15-15  | doi-access = free }}</ref> have all proven useful sources of urease.

== See also ==
*[[Urea carboxylase]]
*[[Allophanate hydrolase]]
*[[Rapid urease test|Urease test]]

== References ==
{{Reflist}}

== External links ==
* {{cite book | vauthors = Mobley HL |title=Helicobacter pylori: Physiology and Genetics | year = 2001 | publisher = ASM Press | location = Washington (DC) | chapter-url = https://www.ncbi.nlm.nih.gov/books/NBK2417/ | veditors=Mobley HL, Mendz GL, Hazell SL | chapter = Chapter 16:Urease | isbn = 978-1-55581-213-3| pmid = 21290719 }}

{{Carbon-nitrogen non-peptide hydrolases}}
{{Enzymes}}
{{Clinical microbiology techniques}}
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[[Category:Nickel enzymes]]
[[Category:EC 3.5.1]]